AMBER: Sander.LES questions

From: Bing Liu <>
Date: Tue, 20 Dec 2005 06:51:09 -0800 (PST)

Dear Amber,
     I try to simulate a protein using Amber 8. This protein has a helix contains 16 residues. That helix orients a quite different position compared with WT because of a single point mutation. I simulated the WT and mutant using both GB and TIP3P model of sander at 310K, but the helix of mutant didn¡¯t make any dramatic move just like that of WT. Then, I try to simulate that phenomenon using sander.LES, but unfortunately, both WT and mutant moved significantly. That wasn¡¯t I wanted. The fact is only the helix of mutant make a large movement. How can I modify the parameters to simulate the fact? I define a region every 3 residues of that helix, 5 copies for each region, using GB model at 310K by sander.LES.
  Your help will be much appreciated! Thanks a lot!
  Bing Liu
  McGill University

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Received on Tue Dec 20 2005 - 15:53:00 PST
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